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DrawPad Free Graphic Design and Drawing Software 6.51 Beta
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Lattice Lut Editor And Viewer 1 8 11
Create bootable USB drives from ISOs with an operating system of your choice, with various options, including to enhance compatibility with old BIOS versions
TeamViewer
Remotely control any PC worldwide, give demonstrations, easily transfer files, host meetings and presentations with multiple users
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Edit videos using three different modes, special effects, transitions and create discs using the built-in burning options that this application provides
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Keep all your installed software applications up to date using this simple app that automatically scans the computer and reveals available updates
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Easily hide important or personal files, folders or even an entire USB Drive with only a few mouse clicks, keeping them safe with a password
Driver Booster PRO
Update all your drivers and game components, thus ensuring your computer runs smoothly and stays issue-free, with this intuitive application
Rufus
Create bootable USB drives from ISOs with an operating system of your choice, with various options, including to enhance compatibility with old BIOS versions
TeamViewer
Remotely control any PC worldwide, give demonstrations, easily transfer files, host meetings and presentations with multiple users
CyberLink PowerDirector
Edit videos using three different modes, special effects, transitions and create discs using the built-in burning options that this application provides
SUMo
Keep all your installed software applications up to date using this simple app that automatically scans the computer and reveals available updates
Wise Folder Hider
Easily hide important or personal files, folders or even an entire USB Drive with only a few mouse clicks, keeping them safe with a password
Driver Booster PRO
Update all your drivers and game components, thus ensuring your computer runs smoothly and stays issue-free, with this intuitive application
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The bioinfomatics software on Bio-Linux consists of the packages below, which includes our own packages as well as bioinformatics packages from the main Debian and Ubuntu repositories. This list was last updated in September 2015 and new and updated packages may have been added since then.
Most of these packages work from the command line, so just type the name of the program to run it, or for R packages activate them using the “library(…)” function. To get more info on a package type “dpkg -s packagename” or to see the local docs for a package type “go /usr/share/doc/packagename“. Clearview 1 9 5 – tabbed style ebook reader. GUI applications can be located through the Installed Applications section of the main Dash menu (the button in the top left corner of the screen).
Package | Version | Description |
---|---|---|
abyss | 1.9.0 | de novo, parallel, sequence assembler for short reads |
ampliconnoise | 1.29 | Programs for the removal of noise from 454 sequenced PCR amplicons |
arb | 5.5 | No description |
archaeopteryx | 0.972.beta9M | A phylogenetic tree viewer and editor |
artemis | 16.0.0 | Free genome viewer and annotation tool |
assembly-conversion-tools | 0.01 | Conversion tools for handling 454 assemblies. |
axiome | 1.7biolinux1 | QIIME and mothur automation toolkit |
axiome-dev | 1.7biolinux1 | QIIME automation toolkit — Plugin Development |
backups | 0.3 | Bio-Linux 5/6/7 backup utilities. |
bamtools | 2.4.0+dfsg | toolkit for manipulating BAM (genome alignment) files |
beam2 | 0.1+20101008 | SNP-SNP interaction association mapping based on SNP-block models |
bedtools | 2.17.0 | suite of utilities for comparing genomic features |
berkeley-express | 1.5.1 | Streaming quantification for high-throughput sequencing |
big-blast | 1.0.3 | The big-blast script for annotation of long sequences |
biocode | 2.3.3 | Biocode plugin for Geneious workbench |
bioperl | 1.6.923 | Perl tools for computational molecular biology |
bioperl-run | 1.6.9 | BioPerl wrappers: scripts |
biosquid | 1.9g+cvs20050121 | utilities for biological sequence analysis |
bitseq | 0.7.0 | Bayesian Inference of Transcripts from Sequencing Data |
blast2 | 1:2.2.26.20120620 | Basic Local Alignment Search Tool |
bldp-files | 1.1 | Documentation for bioinformatics software on Bio-Linux. |
blimps-utils | 3.9 | blocks database improved searcher |
blixem | 3.1.1 | Interactive browser for viewing pairwise Blast results. |
bowtie | 1.1.1 | Ultrafast memory-efficient short read aligner |
bowtie2 | 2.2.6 | ultrafast memory-efficient short read aligner |
bowtie2-debug | 2.2.6 | ultrafast memory-efficient short read aligner |
bwa | 0.7.12 | Burrows-Wheeler Aligner |
cap3 | 20080520 | A base calling system |
catchall | 3.0.1 | Analyze data about microbial species abundance |
cd-hit | 2009-1020 | a suite of programs designed to quickly group sequences |
cdbfasta | 20100722 | Constant DataBase indexing and retrieval tools for multi-FASTA files |
chimeraslayer | 20101212+dfsg | detects likely chimeras in PCR amplified DNA |
clcsequenceviewer | 6.4 | CLC Free Sequence Viewer |
clearcut | 1.0.9 | Relaxed Neighbor Joining |
clustalw | 2.1+lgpl | No description |
clustalx | 2.1+lgpl | No description |
cortex-con | 0.05 | efficient and low-memory software for consensus genome assembly |
cruft-killer | 0.3 | Remove cruft from Bio-Linux desktop |
cufflinks | 2.2.1 | Transcript assembly, differential expression and regulation for RNA-Seq |
cytoscape | 1:3.2.1 | Platform for visualizing complex-networks and integrating these with attribute data |
dendroscope | 1.4.0 | Interactive viewer for large phylogenetic trees. |
dialign | 2.2.1 | Segment-based multiple sequence alignment |
dotter | 3.1 | Graphical dotplot program for detailed comparison of two sequences |
ea-utils | 1.1.2+dfsg | command-line tools for processing biological sequencing data |
embassy-domainatrix | 0.1.650 | Extra EMBOSS commands to handle domain classification file |
embassy-domalign | 0.1.650 | Extra EMBOSS commands for protein domain alignment |
embassy-domsearch | 1:0.1.650 | Extra EMBOSS commands to search for protein domains |
embassy-phylip | 3.69.650 | No description |
emboss | 6.6.0+dfsg | european molecular biology open software suite |
emboss-lib | 6.6.0+dfsg | EMBOSS Libraries |
estscan2 | 2.1 | detects coding regions of DNA sequences |
exchanger | 1.0 | lets you store, annotate and share files via an omixed server |
fasta | 36t2d5 | Collection of programs for searching DNA and protein databases. |
fastdnaml | 1.2.2 | Tool for construction of phylogenetic trees of DNA sequences |
fastqc | 0.11.3 | A quality control application for high throughput sequence data |
fasttree | 2.1.7 | phylogenetic trees from alignments of nucleotide or protein sequences |
fastx-toolkit | 0.0.14 | FASTQ/A short nucleotide reads pre-processing tools |
fixups | 8.0 | Miscellanous fixups for Bio-Linux |
fraggenescan | 1.19 | finds (fragmented) genes in short reads |
galaxy-server | 1.bl.py27.20140730 | Web-based analysis environment for bioinformatics |
galaxy-server-apache-proxy | 1.bl.py27.20140730 | Activates Apache2 proxy for Galaxy server, and PAM authentication |
galaxy-server-pg-database | 1.bl.py27.20140730 | Activates PostgreSQL database back-end for Galaxy |
galaxy-tools-bl | 1:0.5.1 | Standard set of tool wrappers for Galaxy server |
gap2caf | 0.20100408 | Handles conversion of gap format assemblies to caf format. |
geneious | 5.5.7 | Geneious Basic workbench from Biomatters |
geneious-genbanksubmit | 1.3.0 | GenBank submission for Geneious workbench |
genquery | 2.2.4 | GenQuery is a set of Perl libraries for managing SQL query templates and making web-based query forms. |
glam2 | 1:4.10.0.1 | gapped protein motifs from unaligned sequences |
glimmer3 | 3.02 | Gene detection in archea and bacteria |
gnx-tools | 0.1+20120305 | Basic genome assembly statistic tool to calculate Nx values e.g. N50,N10,NG50 |
handlebar | 2.2.2 | Handlebar is a database for storing data about barcodes and acessing the data via a web front-end. |
happy | 1.2 | Multipoint QTL Mapping in Genetically Heterogeneous Animals |
hmmer | 3.1b1 | profile hidden Markov models for protein sequence analysis |
hyphy | 2.1+20111219 | analysis of genetic sequences using multiple techniques |
infernal | 1.1.1 | inference of RNA secondary structural alignments |
isacreator | 1.6.0 | GUI to import and edit ISA dataset descriptions. |
jaligner | 1.0+dfsg | Smith-Waterman algorithm with Gotoh’s improvement |
jalview | 2.8.0b1.dfsg | multiple alignment editor |
jellyfish | 2.2.3 | count k-mers in DNA sequences |
jemboss | 6.6.0+dfsg | graphical user interface to EMBOSS |
jmotu | 1.0.6 | Clusters barcode DNA sequence data into molecular operational taxonomic units |
jprofilegrid | 2.0.5 | Multiple sequence alignment tool that generates ProfileGrids |
keyring | 6 | Public key package for the Bio-Linux package repository |
khmer | 1.1 | k-mer counting, filtering and graph traversal |
khmer-example | 1.1 | k-mer counting, filtering and graph traversal |
last-align | 393 | genome-scale comparison of biological sequences |
lastz | 1.02.00 | Aligns two DNA sequences, inferring appropriate parameters automatically |
libbiojava-java | 1:1.7.1 | Java API to biological data and applications (default version) |
libbiojava-java-demos | 1:1.7.1 | Example programs for BioJava |
libpandaseq-sam1 | 1.2~ppa0 | Pair-end read assembler |
libpandaseq-url0 | 2.7~ppa0 | Pair-end read assembler — URL handler |
libpandaseq5 | 2.7~ppa0 | Pair-end read assembler |
lucy | 1.19p | Preparation of raw DNA sequence fragments for sequence assembly |
macs14 | 1.4.2.1 | Model-based Analysis of ChIP-Seq on short reads sequencers |
mafft | 7.215 | Multiple alignment program for amino acid or nucleotide sequences |
maq | 0.7.1 | maps short fixed-length polymorphic DNA sequence reads to reference sequences |
maxd | 2.3.0 | maxd is a data warehouse and visualisation environment for genomic expression data. |
mdust | 1:0.1+20020708 | repetitive sequence masker |
meme | 1:4.10.0.1 | search for common motifs in DNA or protein sequences |
mesquite | 2.74 | Software for evolutionary biology. |
metavelvet | 1.2.02 | extension of Velvet assembler to de novo metagenomic assembly |
microbiomeutil | 20101212+dfsg | Microbiome Analysis Utilities |
mira-3rdparty | 20120706 | Additional useful tools to accomapany the MIRA assembler |
mira-assembler | 4.9.5 | Whole Genome Shotgun and EST Sequence Assembler |
mothur | 1.36.1+dfsg | sequence analysis suite for research on microbiota |
mothur-lookup-files | 1 | .pat lookup files for Mothur |
mothur-mpi | 1.36.1+dfsg | mpi-enabled binary for mothur |
mrbayes-mpi | 3.2.2+dfsg | Bayesian Inference of Phylogeny – mpi version |
msatfinder | 2.0.10 | Microsatellite Finder |
mspcrunch | 2.5 | a BLAST post-processing filter. |
mummer | 3.23~dfsg | Efficient sequence alignment of full genomes |
muscle | 1:3.8.31 | Multiple alignment program of protein sequences |
mview | 1.51 | Multiple alignment viewer for sequence database search results. |
natefoo-add-scores | 0.1+20101006 | small helper application used by Galaxy server |
natefoo-taxonomy | 0.1+20101102 | small taxonomy applications used by Galaxy server |
ncbi-blast+ | 2.2.28 | next generation suite of BLAST sequence search tools |
ncbi-blast+-legacy | 2.2.28 | NCBI Blast legacy call script |
ncbi-seg | 0.0.20000620 | tool to mask segments of low compositional complexity in amino acid sequences |
ncbi-tools-bin | 6.1.20120620 | NCBI libraries for biology applications (text-based utilities) |
ncbi-tools-x11 | 6.1.20120620 | NCBI libraries for biology applications (X-based utilities) |
njplot | 2.4 | phylogenetic tree drawing program |
nrdb | 2 | Generates quasi-nonredundant protein and nucleotide sequence databases |
ocount | 0.5 | Oligonucleotide frequency counter |
oligoarray | 2.1 | Computes oligonucleotides for microarray construction |
oligoarrayaux | 3.7 | Free software that is required for the OligoArray2.1 software. |
omegamap | 0.5 | Detects natural selection and recombination in DNA or RNA sequences. |
paml | 4.7 | Phylogenetic Analysis by Maximum Likelihood (PAML) |
pandaseq | 2.7~ppa0 | Pair-end read assembler |
pandaseq-dev | 2.7~ppa0 | Pair-end read assembler — Development tools |
pandaseq-sam | 1.2~ppa0 | Pair-end read assembler |
pandaseq-sam-dev | 1.2~ppa0 | Pair-end read assembler — Development tools |
parafly | 0.0.2013.01.21 | parallel command processing using OpenMP |
parsinsert | 1.04 | Parsimonious Insertion of unclassified sequences into phylogenetic trees |
pass2 | 0.1+20101008 | Peak calling in ChIP data based on Poisson de-clumping |
perm | 0.4.0 | Efficient mapping of short reads with periodic spaced seeds |
pfaat | 1.0.034 | Sequence alignment editor designed for protein family analysis. |
phylip | 1:3.695 | No description |
phyml | 2:20120412 | Phylogenetic estimation using Maximum Likelihood |
picard-tools | 1.105 | Command line tools to manipulate SAM and BAM files |
plymouth-theme | 8.2 | Boot splash for Bio-Linux 8 |
prank | 0.0.140110 | Probabilistic Alignment Kit for DNA, codon and amino-acid sequences |
predictprotein | 1.0.94 | suite of protein sequence analysis tools |
priam | 2005.07 | Generate enzyme-specific profiles for metabolic pathyway prediction |
primer3 | 2.3.6 | Tool to design flanking oligo nucleotides for DNA amplification |
probcons | 1.12 | PROBabilistic CONSistency-based multiple sequence alignment |
pymol | 1.7.2.1 | Molecular Graphics System |
qiime | 1.9.1+dfsg | Quantitative Insights Into Microbial Ecology |
qiime-default-reference | 0.1.3 | QIIME default reference dataset |
qtlcart | 1.17f | Map quantitative traits using a map of molecular markers. |
r-base | 3.2.2 | GNU R statistical computation and graphics system |
r-base-core | 3.2.2 | GNU R core of statistical computation and graphics system |
r-base-dev | 3.2.2 | GNU R installation of auxiliary GNU R packages |
r-bioc-affy | 1.46.1 | GNU R package “Methods for Affymetrix Oligonucleotide |
r-bioc-affyio | 1.36.0 | GNU R package “Tools for parsing Affymetrix data files” |
r-bioc-annotate | 1.42.0 | GNU R package “Annotation for microarrays” |
r-bioc-annotationdbi | 1.26.0 | GNU R package “Annotation Database Interface” |
r-bioc-biobase | 2.28.0 | GNU R package “Biobase: Base functions for Bioconductor” |
r-bioc-biocgenerics | 0.14.0 | GNU R package “S4 generic functions for Bioconductor” |
r-bioc-biocinstaller | 1.18.4 | GNU R package “Install/Update Bioconductor and CRAN |
r-bioc-biocparallel | 1.2.9 | GNU R package “Bioconductor facilities for parallel |
r-bioc-biomart | 2.18.0 | GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene) |
r-bioc-biostrings | 2.36.4 | GNU R package “String objects representing biological |
r-bioc-bitseq | 1.8.0 | Bioconductor package “Transcript expression inference and differential |
r-bioc-deseq | 1.16.0 | Differential gene expression analysis based on the -ve binomial distribn. |
r-bioc-edger | 3.6.2 | GNU R package “Empirical analysis of digital gene |
r-bioc-genefilter | 1.46.1 | GNU R package “genefilter: methods for filtering genes |
r-bioc-geneplotter | 1.42.0 | Graphics related functions for Bioconductor |
r-bioc-genomeinfodb | 1.4.2 | GNU R package “Utilities for manipulating chromosome and |
r-bioc-genomicalignments | 1.4.1 | GNU R package “Representation and manipulation of short |
r-bioc-genomicranges | 1.20.6 | GNU R package “Representation and manipulation of genomic |
r-bioc-hilbertvis | 1.23.0 | GNU R package to visualise long vector data |
r-bioc-impute | 1.38.1 | GNU R package “impute: Imputation for microarray data” |
r-bioc-iranges | 2.2.7 | GNU R package “Infrastructure for manipulating intervals |
r-bioc-limma | 3.20.5 | GNU R package “Linear Models for Microarray Data” |
r-bioc-multtest | 2.24.0 | GNU R package “Resampling-based multiple hypothesis |
r-bioc-pcamethods | 1.54.0 | Bioconductor “pcaMethods: A collection of PCA methods.” |
r-bioc-preprocesscore | 1.30.0 | GNU R package “A collection of pre-processing functions” |
r-bioc-qvalue | 1:1.38.0 | Bioconductor package “Q-value estimation for false discovery rate control” |
r-bioc-rsamtools | 1.20.4 | GNU R package “Binary alignment (BAM), variant call (BCF), |
r-bioc-s4vectors | 0.6.5 | GNU R package “S4 implementation of vectors and lists” |
r-bioc-xvector | 0.8.0 | GNU R package “Representation and manpulation of external |
r-bioc-zlibbioc | 1.10.0 | GNU R package “An R packaged zlib-1.2.5” |
r-cran-abind | 1.4-0 | GNU R package “Combine multi-dimensional arrays” |
r-cran-ade4 | 1.7-2 | GNU R package “Analysis of Ecological Data : Exploratory |
r-cran-ape | 3.3 | GNU R package “Analyses of Phylogenetics and Evolution” |
r-cran-aplpack | 1.3.0 | GNU R package “Another Plot PACKage: stem.leaf, bagplot, |
r-cran-bitops | 1.0-6 | GNU R package implementing bitwise operations |
r-cran-catools | 1.17.1 | GNU R package “Tools: moving window statistics, GIF, |
r-cran-cluster | 2.0.3 | GNU R package for cluster analysis by Rousseeuw et al |
r-cran-data.table | 1.9.4 | GNU R package “Extension of data.frame” |
r-cran-dbi | 0.3.1 | GNU R package “R Database Interface” |
r-cran-dichromat | 2.0.0 | Color schemes for dichromats |
r-cran-digest | 0.6.8 | GNU R package “Create Cryptographic Hash Digests of R |
r-cran-evaluate | 0.7.2 | GNU R package “Parsing and Evaluation Tools that Provide |
r-cran-futile.logger | 1.4.1 | GNU R package “A Logging Utility for R” |
r-cran-futile.options | 1.0.0 | GNU R package “Futile options management” |
r-cran-gdata | 2.17.0 | GNU R package “Various R Programming Tools for Data |
r-cran-gee | 4.13-19 | GNU R package “Generalized Estimation Equation Solver” |
r-cran-getopt | 1.20.0 | GNU R package “C-like getopt behavior.” |
r-cran-ggplot2 | 1.0.1 | GNU R package “An Implementation of the Grammar of |
r-cran-gplots | 2.17.0 | GNU R package “Various R Programming Tools for Plotting |
r-cran-gtable | 0.1.2 | GNU R package “Arrange grobs in tables.” |
r-cran-gtools | 3.5.0 | GNU R package “Various R Programming Tools” |
r-cran-labeling | 0.3 | GNU R package “Axis Labeling” |
r-cran-lambda.r | 1.1.7 | GNU R package “Modeling Data with Functional Programming” |
r-cran-lattice | 0.20-29 | GNU R package “Lattice Graphics” |
r-cran-leaps | 2.9 | GNU R package “regression subset selection” |
r-cran-lme4 | 1.1-9 | GNU R package for linear mixed effects model fitting |
r-cran-locfit | 1.5-9.1 | Local Regression, Likelihood and Density Estimation. |
r-cran-matrix | 1.2-2 | GNU R package of classes for dense and sparse matrices |
r-cran-matrixstats | 0.10.0 | R package “Methods that apply to rows and columns of a matrix” |
r-cran-munsell | 0.4.2 | GNU R package “Munsell colour system” |
r-cran-nlme | 3.1.122 | GNU R package for (non-)linear mixed effects models |
r-cran-optparse | 1.2.0 | GNU R package “Command line option parser.” |
r-cran-permute | 0.8-4 | GNU R package “Functions for Generating Restricted |
r-cran-plotrix | 3.5-7 | GNU R package “Various plotting functions” |
r-cran-plyr | 1.8.3 | GNU R package “Tools for Splitting, Applying and Combining |
r-cran-prettyr | 2.0-8 | GNU R package “Pretty descriptive stats.” |
r-cran-propcis | 0.2-5 | GNU R package “PropCIs: Various confidence interval methods for proportions” |
r-cran-proto | 0.3-10 | GNU R package “Prototype object-based programming” |
r-cran-r.methodss3 | 1.6.1 | GNU R package “Utility function for defining S3 methods” |
r-cran-rapidr | 0.1.1 | GNU R package “RAPIDR: Reliable Accurate Prenatal non-Invasive Diagnosis.” |
r-cran-rcolorbrewer | 1.0-5 | GNU R package providing suitable color palettes |
r-cran-rcpp | 0.12.1 | GNU R package “Seamless R and C++ Integration” |
r-cran-rcurl | 1.95-4.7 | GNU R package “General Network (HTTP/FTP/…) Client |
r-cran-relimp | 1.0-4 | GNU R package “Relative Contribution of Effects in a |
r-cran-reshape2 | 1.4.1 | GNU R package “Flexibly Reshape Data: A Reboot of the |
r-cran-rggobi | 2.1.20 | GNU R package for the GGobi data visualization system |
r-cran-rgl | 0.95.1247 | GNU R package for three-dimensional visualisation using OpenGL |
r-cran-rgtk2 | 2.20.31 | GNU R binding for Gtk2 |
r-cran-rmpi | 0.6-5 | GNU R package interfacing MPI libraries for distributed computing |
r-cran-rserve | 1.7-3 | GNU R Rserve tcp/ip server and sample clients |
r-cran-rsqlite | 1.0.0 | GNU R package “SQLite Interface for R” |
r-cran-rwave | 2.4 | GNU R package “Time-Frequency Analysis of 1-D Signals” |
r-cran-samr | 2.0 | GNU R package “SAM: Significance Analysis of Microarrays” |
r-cran-scales | 0.3.0 | GNU R package “Scale Functions for Visualization” |
r-cran-scatterplot3d | 0.3-36 | GNU R package “3D Scatter Plot” |
r-cran-snowfall | 1.84-6 | GNU R package “Easier cluster computing (based on snow).” |
r-cran-sp | 1:1.1-0 | GNU R package “Classes and Methods for Spatial Data” |
r-cran-stringr | 1.0.0 | GNU R package “Simple, Consistent Wrappers for Common |
r-cran-tcltk2 | 1.2-9 | GNU R package “Tcl/Tk Additions” |
r-cran-testthat | 0.9.1 | GNU R package “Testthat code. Tools to make testing fun |
r-cran-vegan | 2.3-0 | GNU R package “Community Ecology Package” |
r-cran-waveslim | 1.7.5 | GNU R package “Basic wavelet routines for one-, two- and |
r-cran-wavethresh | 4.6.6 | GNU R package “Wavelets statistics and transforms.” |
r-cran-xml | 3.98-1.3 | GNU R package “Tools for Parsing and Generating XML Within |
r-cran-xtable | 1:1.7-3 | GNU R coerce data to LaTeX and HTML tables |
r-mathlib | 3.2.2 | GNU R standalone mathematics library |
r-recommended | 3.2.2 | GNU R collection of recommended packages [metapackage] |
rasmol | 2.7.5.2 | Visualize biological macromolecules |
raxml | 8.0.26 | Randomized Axelerated Maximum Likelihood of phylogenetic trees |
ray | 2.3.1 | parallel de novo genome assemblies of next-gen sequencing data |
ray-extra | 2.3.1 | Scripts and XSL sheets for post-processing for ray de novo assembler |
rbs-finder | 1.0 | A program to find Ribosomal binding sites. |
rdp-classifier | 2.10.2+dfsg | taxonomic assignment from next generation sequencing |
readseq | 1 | Conversion between sequence formats |
rsem | 1.2.22+dfsg | RNA-Seq by Expectation-Maximization |
sampledata | 20041011 | Sample data for Bio-Linux packages |
samtools | 0.1.19 | processing sequence alignments in SAM and BAM formats |
scythe | 0.993 | Bayesian adapter trimmer for nextgen sequence reads |
seaview | 1:4.4.2 | No description |
seqprep | 1.1 | tool for stripping adaptors and/or merging paired reads with overlap |
shared | 1.1 | Some shared files used by Bio-Linux |
sickle | 1.33 | windowed adaptive trimming tool for FASTQ files using quality |
sift | 4.0.3b | predicts if a substitution in a protein has a phenotypic effect |
sortmerna | 2.0 | tool for filtering, mapping and OTU-picking NGS reads |
splitstree | 4.12.6 | Analysis and visualisation tool for distance data from biological sequences |
sputnik-mononucleotide | 0.1+20101005 | Searches DNA sequence files in FASTA format for microsatellite repeats |
squint | 1.02 | Java-based multiple alignment program and editor |
ssake | 3.8.1 | genomics application for assembling millions of very short DNA sequences |
stacks | 1.34 | pipeline for building loci from short-read sequences |
stacks-web | 1.34 | web interface for displaying loci from short-read sequences |
staden | 2.0.0b10 | DNA sequence assembly (Gap4/Gap5), editing and analysis tools |
staden-common | 2.0.0b10 | Architecture independent files for Staden |
stars | 1.2a | STARS is an alternative interface to Staden. |
sumatra | 1.0.01 | fast and exact comparison and clustering of sequences |
swarm | 1.2.20 | robust and fast clustering method for amplicon-based studies |
t-coffee | 10.00.r1613 | Multiple Sequence Alignment |
tablet | 1.14.04.10 | Graphical viewer for next gen sequence assemblies and alignments |
taxinspector | 1.0b3 | Browser for entries in the NCBI taxonomy database |
tetra | 1.0b3 | tetranucleotide frequency calculator with GUI |
themes-v7 | 7.0 | Graphics, icons, wallpaper and desktop settings for Bio-Linux 7 |
themes-v8 | 8.0 | Graphics, icons, wallpaper and desktop settings for Bio-Linux 8 |
tophat | 2.1.0 | fast splice junction mapper for RNA-Seq reads |
trace2dbest | 3.14 | Processes trace files into dbEST submissions |
transdecoder | 2.0.1+dfsg | find coding regions within transcripts |
transterm-hp | 2.07 | Transterm finds rho-independent transcription terminators in bacterial genomes. |
transtermhp | 2.09 | find rho-independent transcription terminators in bacterial genomes |
tree-puzzle | 5.2 | Reconstruction of phylogenetic trees by maximum likelihood |
tree-puzzle-doc | 5.2 | Reconstruction of phylogenetic trees by maximum likelihood |
treeviewx | 0.5.1+20100823 | Displays and prints phylogenetic trees |
trinityrnaseq | 2.0.6+dfsg | RNA-Seq De novo Assembly |
trinityrnaseq-sampledata | 2.0.6+dfsg | RNA-Seq De novo Assembly |
trnascan | 1.23 | tRNAscan-SE searches for tRNA genes in genomic sequences. |
trnascan-se | 1.3.1 | search for tRNA genes in genomic sequences |
tutorials | 1 | Tutorials and documentation for Bio-Linux users. |
ugene | 1.18.0+repack | integrated bioinformatics toolkit |
unity-lens | 0.2 | unity lens for Bio-Linux |
usb-maker | 8.2 | Script to generate Bio-Linux live memory sticks. |
velvet | 1.2.10+dfsg | Nucleic acid sequence assembler for very short reads |
velvet-example | 1.2.10+dfsg | Example data for the Velvet sequence assembler |
velvet-long | 1.2.10+dfsg | Nucleic acid sequence assembler for very short reads, long version |
velvetoptimiser | 2.2.5 | Automatically optimise Velvet do novo assembly parameters |
vsearch | 1.1.1.nodata | tool for processing metagenomic sequences |
weblogo | 3.3 | create sequence logos from biological sequence alignments |
wise | 2.4.1 | comparison of biopolymers, commonly DNA and protein sequences |
xcut | 1.4.2 | A re-write of the GNU cut command with many new features. |
zsh | 1 | Z-Shell wrapper package for Bio-Linux. |